Cette thèse consiste en l'utilisation d'outils d'informatiques pour recueillir des informations concernant l'écologie d'espèces animales. L'objectif de départ était d'assembler des algorithmes capables de traiter des enregistrements acoustiques et de détecter, lister et dénombrer les sons éventuellement présents d'insectes, amphibiens et oiseaux. Pour ce faire nous avons testé de manière non exhaustive différents classifieurs et descripteurs de signal audio9 pour (première partie) organiser et participer à trois concours internationaux de reconnaissance automatique de sons d'animaux et (seconde partie) construire un outil de suivi d'abondance de deux espèces d'oiseaux marins pélagiques sur l'île de la Réunion. La première moitié de la thèse (chapitre 7) a été dédiée à la construction et au test de modèles de reconnaissance multi-classes (92 espèces animales : 82 espèces d'oiseaux (dont 66 passériformes), 9 espèces d'insectes, et 1 espèce d'amphibien, Pelophylax kl. grafi). La seconde moitié de la thèse (chapitre 8) s'est concentrée sur la construction de détecteurs de cris de deux espèces d'oiseaux protégées dont les colonies sont particulièrement difficiles d'accès et menacées par le développement et les éclairages urbains : Le Pétrel de Barau (Pterodroma baraui, endémique de la Réunion et en danger d'extinction depuis 2008 d'après l'UICN) et le Puffin tropical (Puffinus bailloni). / The present manuscript deals with computer science applied to ecology. The main objective was to assembly algorithms able to analyse acoustic recordings and automatically detect, list and count sounds of insects, amphibiansand birds. We tested a non exhaustive list of audio features and classifiers to (first part) organize and participate to three international challenges of automatic regnotion of animal's sounds and (second part) build a automatic and passive acoustic monitoring of two species of pelagic seabirds on the Reunion island.

Nightjars are a group of nocturnal and aerial insectivorous birds that have experienced long-term decline likely driven primarily by habitat loss and declines in prey populations. Eastern Whip-poor-will (Antrostomus vociferus) and Chuck-will’s-widow (Antrostomus carolinensis), two nightjar species native to Illinois, declined 69% and 58% since 1966, respectively. Although previous survey efforts have documented presence of Chuck-will’s-widow and Whip-poor-will, their current distribution in the state is not well known. Using Autonomous Recording Units (ARUs) deployed in a uniform, systematic grid, I surveyed 142 locations from May – July 2022 on public and private lands across the southern eleven counties of Illinois to assess Whip-poor-will and Chuck-will’s-widow distribution and estimate species occupancy. I estimated species relationships with proportion of landcover types, forest patch configuration, and proximity to other landcover types. Additionally, I quantified disturbances from the past 15 years to estimate species relationships to the severity and duration of disturbances. I deployed ARUs for 710 survey days collecting 170,400 minutes or 3,000 hours of recordings. Acoustic bird call identification software, BirdNet, was highly accurate at detecting focal species and greatly reduced the time spent manually reviewing acoustic data. BirdNet identified 43,922 calls of Whip-poor-will and 31,447 calls of Chuck-will’s-widow. I detected Whip-poor-will on 78 surveys with 100% accuracy and Chuck-will’s-widow on 75 surveys with 76% accuracy. Whip-poor-will were positively associated with forest patches with large core areas that neighbored pastures. Additionally, Whip-poor-will were likely to occupy landscapes that had experienced low to moderate disturbance within the previous 15 years. Covariates used to model Chuck-will’s-widow occupancy explained little variation in detection or occupancy and there were no significant relationships with any covariate. However, examining non-significant trends suggest similar relationships as Whip-poor-will in the area. Results highlight the efficiency of passive acoustic monitoring for these birds and the need for further investigation into Chuck-will’s-widow species-environmental relationships. In southern Illinois, Chuck-will’s-widow populations appears to be consistent with previous estimates from the 1990s while Whip-poor-will follow the broader trend of decline.